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feat(bentoctl): add global CLI access with shell autocompletions #331

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52a6fe5
feat(bentoctl): add global CLI access with shell autocompletions
SanjeevLakhwani Nov 18, 2025
dc44ac9
docs: add bash completion script and expand installation docs
SanjeevLakhwani Nov 19, 2025
0b01d06
perf(bentoctl): optimize imports for faster tab completions
SanjeevLakhwani Nov 19, 2025
80f0794
style(bentoctl): fix flake8 lint issues
SanjeevLakhwani Nov 19, 2025
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39 changes: 39 additions & 0 deletions bin/bentoctl
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#!/usr/bin/env bash
# bentoctl - Global wrapper to run bentoctl from anywhere
#
# This script allows you to invoke bentoctl from any directory.
# It changes to the BENTO_HOME directory and runs the actual bentoctl.bash script.

# Determine the Bento installation directory
# If BENTO_HOME is set, use it; otherwise, use the script's parent directory
if [[ -z "${BENTO_HOME}" ]]; then
# Get the directory where this script is located (resolving symlinks)
SCRIPT_PATH="$(readlink -f "${BASH_SOURCE[0]}")"
BENTO_HOME="$(dirname "$(dirname "$SCRIPT_PATH")")"
fi

export BENTO_HOME

# Validate that the directory exists
if [[ ! -d "${BENTO_HOME}" ]]; then
echo "Error: BENTO_HOME directory not found: ${BENTO_HOME}" >&2
echo "Set BENTO_HOME environment variable to your bento installation path." >&2
exit 1
fi

# Validate that bentoctl.bash exists
if [[ ! -f "${BENTO_HOME}/bentoctl.bash" ]]; then
echo "Error: bentoctl.bash not found in ${BENTO_HOME}" >&2
exit 1
fi

# Change to the Bento directory and execute the script
cd "${BENTO_HOME}" || exit 1

# Activate virtual environment if it exists
if [[ -f "${BENTO_HOME}/env/bin/activate" ]]; then
source "${BENTO_HOME}/env/bin/activate"
fi

# Execute the actual bentoctl script with all arguments
exec ./bentoctl.bash "$@"
176 changes: 176 additions & 0 deletions completions/_bentoctl
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#compdef bentoctl

# Zsh completion script for bentoctl
# Place this file in a directory in your $fpath (e.g., ~/.zsh/completions/)
# Or source it directly in your .zshrc

_bentoctl() {
local curcontext="$curcontext" state line
typeset -A opt_args

local -a commands
commands=(
# Initialization commands
'init-dirs:Initialize directories for BentoV2 structure'
'init-auth:Configure authentication with Keycloak'
'init-certs:Initialize SSL certificates for gateway domains'
'init-docker:Initialize Docker configuration and networks'
'init-web:Initialize web app (public or private) files'
'init-all:Initialize certs, directories, Docker networks, and web portals'
'init-config:Initialize configuration files for specific services'
'init-cbioportal:Initialize cBioPortal if enabled'

# Database commands
'pg-dump:Dump contents of all Postgres databases to a directory'
'pg-load:Load contents of all Postgres databases from a directory'

# Utility commands
'convert-pheno:Convert a Phenopacket V1 JSON document to V2'
'conv:Convert a Phenopacket V1 JSON document to V2'

# Service commands
'run:Run Bento services'
'start:Run Bento services'
'up:Run Bento services'
'stop:Stop Bento services'
'down:Stop Bento services'
'restart:Restart Bento services'
'clean:Clean services'
'work-on:Work on a service in local development mode'
'dev:Work on a service in local development mode'
'develop:Work on a service in local development mode'
'local:Work on a service in local development mode'
'prebuilt:Switch a service back to prebuilt mode'
'pre-built:Switch a service back to prebuilt mode'
'prod:Switch a service back to prebuilt mode'
'mode:See service production/development mode'
'state:See service production/development mode'
'status:See service production/development mode'
'pull:Pull the image for a specific service'
'shell:Run a shell inside a running service container'
'sh:Run a shell inside a running service container'
'run-as-shell:Run a shell inside a stopped service container'
'logs:Check logs for a service'
'compose-config:Generate Compose config YAML'
)

# Common services for service-based commands
local -a all_services
all_services=(
'all:All services'
'aggregation:Federation/aggregation service'
'auth:Authentication service'
'auth-db:Authentication database'
'authz:Authorization service'
'authz-db:Authorization database'
'beacon:Beacon service'
'cbioportal:cBioPortal service'
'drs:Data Repository Service'
'drop-box:Drop box service'
'event-relay:Event relay service'
'gateway:Gateway/proxy service'
'gohan:Gohan services (api + elasticsearch)'
'gohan-api:Gohan API service'
'gohan-elasticsearch:Gohan Elasticsearch'
'katsu:Metadata service'
'katsu-db:Metadata database'
'notification:Notification service'
'public:Public frontend'
'redis:Redis cache'
'reference:Reference service'
'reference-db:Reference database'
'service-registry:Service registry'
'web:Web frontend'
'wes:Workflow Execution Service'
)

# Services that can be worked on (have repositories)
local -a workable_services
workable_services=(
'aggregation:Federation/aggregation service'
'authz:Authorization service'
'beacon:Beacon service'
'drs:Data Repository Service'
'drop-box:Drop box service'
'event-relay:Event relay service'
'gateway:Gateway service'
'gohan-api:Gohan API service'
'katsu:Metadata service'
'notification:Notification service'
'public:Public frontend'
'reference:Reference service'
'service-registry:Service registry'
'web:Web frontend'
'wes:Workflow Execution Service'
)

_arguments -C \
'(-d --debug)'{-d,--debug}'[Enable remote Python debugging]' \
'1: :->command' \
'*:: :->args'

case $state in
command)
_describe -t commands 'bentoctl command' commands
;;
args)
case $line[1] in
run|start|up|stop|down|restart|clean|logs|pull|mode|state|status)
_arguments \
'1: :->service' \
'(-p --pull)'{-p,--pull}'[Pull the service image first]' \
'(-f --follow)'{-f,--follow}'[Follow logs]'
if [[ $state == service ]]; then
_describe -t services 'service' all_services
fi
;;
work-on|dev|develop|local)
_arguments '1: :->service'
if [[ $state == service ]]; then
_describe -t services 'service' workable_services
fi
;;
prebuilt|pre-built|prod)
_arguments '1: :->service'
if [[ $state == service ]]; then
_describe -t services 'service' all_services
fi
;;
shell|sh|run-as-shell)
_arguments \
'1: :->service' \
'(-s --shell)'{-s,--shell}'[Shell to use]: :(/bin/bash /bin/sh)'
if [[ $state == service ]]; then
_describe -t services 'service' all_services
fi
;;
init-web)
_arguments \
'1: :(public private)' \
'(-f --force)'{-f,--force}'[Overwrite existing files]'
;;
init-config)
_arguments \
'1: :(katsu beacon beacon-network)' \
'(-f --force)'{-f,--force}'[Overwrite existing config]'
;;
init-certs)
_arguments '(-f --force)'{-f,--force}'[Remove and recreate certificates]'
;;
pg-dump|pg-load)
_arguments '1:directory:_directories'
;;
convert-pheno|conv)
_arguments \
'1:source file:_files -g "*.json"' \
'2:target file:_files -g "*.json"'
;;
compose-config)
_arguments '--services[List services seen by Compose]'
;;
esac
;;
esac
}

_bentoctl "$@"
72 changes: 72 additions & 0 deletions completions/bentoctl.bash
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# Bash completion script for bentoctl
# Place this file in /etc/bash_completion.d/ or ~/.local/share/bash-completion/completions/

_bentoctl_completions() {
local cur prev words cword
_init_completion || return

local commands="init-dirs init-auth init-certs init-docker init-web init-all init-config init-cbioportal pg-dump pg-load convert-pheno conv run start up stop down restart clean work-on dev develop local prebuilt pre-built prod mode state status pull shell sh run-as-shell logs compose-config"

# All services (for most commands)
local all_services="all aggregation auth auth-db authz authz-db beacon cbioportal drs drop-box event-relay gateway gohan gohan-api gohan-elasticsearch katsu katsu-db notification public redis reference reference-db service-registry web wes"

# Services that can be worked on (have repositories)
local workable_services="aggregation authz beacon drs drop-box event-relay gateway gohan-api katsu notification public reference service-registry web wes"

if [[ ${cword} -eq 1 ]]; then
COMPREPLY=($(compgen -W "${commands}" -- "${cur}"))
return
fi

case "${prev}" in
run|start|up|stop|down|restart|clean|logs|pull|mode|state|status)
COMPREPLY=($(compgen -W "${all_services}" -- "${cur}"))
;;
work-on|dev|develop|local)
COMPREPLY=($(compgen -W "${workable_services}" -- "${cur}"))
;;
prebuilt|pre-built|prod)
COMPREPLY=($(compgen -W "${all_services}" -- "${cur}"))
;;
shell|sh|run-as-shell)
COMPREPLY=($(compgen -W "${all_services}" -- "${cur}"))
;;
init-web)
COMPREPLY=($(compgen -W "public private" -- "${cur}"))
;;
init-config)
COMPREPLY=($(compgen -W "katsu beacon beacon-network" -- "${cur}"))
;;
pg-dump|pg-load)
_filedir -d
;;
convert-pheno|conv)
_filedir
;;
-s|--shell)
COMPREPLY=($(compgen -W "/bin/bash /bin/sh" -- "${cur}"))
;;
*)
# Handle flags
case "${words[1]}" in
run|start|up|restart)
COMPREPLY=($(compgen -W "-p --pull" -- "${cur}"))
;;
logs)
COMPREPLY=($(compgen -W "-f --follow" -- "${cur}"))
;;
init-certs|init-web|init-config)
COMPREPLY=($(compgen -W "-f --force" -- "${cur}"))
;;
shell|sh|run-as-shell)
COMPREPLY=($(compgen -W "-s --shell" -- "${cur}"))
;;
compose-config)
COMPREPLY=($(compgen -W "--services" -- "${cur}"))
;;
esac
;;
esac
}

complete -F _bentoctl_completions bentoctl
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